This game's version of Green Hill Zone has an expansive, flooded underground area, similar to the Master System/Game Gear version of the first Sonic game.

At one point Sonic repeats a line almost directly from Sonic Colors:

(In Colors) Cubot: "Your plans have been crushed by Sonic for, like ever. He stops you like it's his job or something."
(In Generations) Sonic: "Seriously, we beat this guy every time. It's like it's our job or something."

Some characters appear in stages that they were in previously. To list:

At the end of the game, it is revealed that Generations is the direct sequel to Sonic Colors. To be more precise, Eggman explains that he found the Time Eater immediately after The Stinger of Colors.

In the English pre-final boss cutscene, Classic Tails refers to Classic Eggman as "Dr. Robotnik", then Classic Eggman corrects Classic Tails, stating that nobody calls him by his real name anymore.

At the end of Sonic Adventure, Sonic says to Perfect Chaos "Hey, I'll play with you some other time."

When Rouge and Shadow appear to cheer Sonic on before fighting the Time Eater, Classic Eggman asks who they are, since he hasn't met them yet.

Modern Sonic first gets a tutorial on Light Dashing in Speed Highway -- Sonic Adventure was the first game to give Sonic that ability. On the same note, the first tutorial on walljumping is in Seaside Hill, which gave the 'speed' member of each team[7] a walljumping ability -- including Sonic.

The final boss is revealed to be a creature having turned manned machine by the combined efforts of Classic and Modern Eggman, which makes sense when you remember all the classic Mooks Eggman built were powered by animals he captured.

After the credits, Classic Eggman and Modern Eggman are arguing when Classic Eggman asks "Do we ever win?", Modern Eggman responds "That depends on your definition of 'win'". As Eggman did win in Sonic Riders, but he only won a carpet.

This is followed up by Classic Robotnik considering going for a teaching degree, a possible nod to Sonic's Schoolhouse, in which he appears.

A subtle one occurs within the levels. The springboard from Sonic the Hedgehog 2 appears in this game, in Classic Sonic's stages. What should be noticed is that Green Hill (the level from Sonic 1) is the only level that doesn't seem to have them, while it was introduced in Chemical Plant (the level from Sonic the Hedgehog 2).

There's also a small one in the cutscene where Sonic finds Knuckles-- who immediately preforms a watered-down version of the Spiral Upper upon being unfrozen.

↑The original version has Knuckles help Sonic & Tails get to the Death Egg from there. It was also the location of Knuckles' Final Boss.

↑While Rouge isn't playable in the original City Escape, the level's debut, Sonic Adventure 2, is also still her debut.

↑However, Cheese is a Chao and the first debut the Chao made were in Sonic Adventure.